(From the Facebook page, The Power of Nam Myoho Renge Kyo, quoting from the Wisdom of The Lotus Sutra)

In this Q & A, President Ikeda clarifies and explains on extraneous thoughts that come to our mind while chanting :

Endo: With regard to prayer, people frequently bring up 

President Ikeda:
There is nothing wrong with having an active mind while chanting.
This is a natural human tendency.

The important thing is to face the Gohonzon just as we are,
without affectation.
Having extraneous thoughts is an inherent part of our lives
in that we are entities of the principle of three thousand realms in a single moment of life.
Therefore, through daimoku we can turn even those thoughts into benefit.

There are no rules governing how we should pray.
There’s no need to be something we aren’t.
Even if we were to try to control our thoughts
by making our prayer rigid and forced,
our minds would still tend to wander.
As we deepen our faith, we also strengthen our ability to concentrate.

Actually, since the thoughts or ideas that come to mind as we chant r
epresent issues that concern us at the moment,
we should not consider them extraneous.
Instead, we should pray earnestly about each one,
whatever it may be.
Rather than chant only about large issues,
we should pray specifically about every issue we face,
winning over each one and strengthening our foundation as we go.
There is of course no need to be tense or nervous when praying. What matters is that we are completely ourselves.

(The Wisdom of the Lotus Sutra, Vol. VI pp. 108-09)
Thanks Jamie Lee Silver!